The angry statement followed weeks of speculation on Internet social networks of a split between the “jihadist” allies.
Al-Nusra "completely denies reports of a break-up with Al-Qaeda," the group said in a statement released on Twitter.
It said Al-Nusra "remains the backbone of jihadists" in Syria, "the first into battle, dedicated to unifying the ranks around sharia (Islamic law)... righting injustice and defending the disadvantaged".
It denied "completely all reports of a meeting with Qatari or other intelligence services or seeking Qatari or Persian Gulf funding, as this is contrary to the principles on which Al-Nusra has been based from the start".
An official branch of Al-Qaeda since April 2013, the group dominates a swathe of northwest Syria despite months of US-led coalition airstrikes, AFP reports.
The idea of a split with Al-Qaeda emerged in early 2014 when Al-Nusra militants in the eastern province of Deir Ezzor allied with anti-army rebels supported by the West and oil-rich Persian Gulf monarchies in the face of gains by IS.
Al-Nusra was formed in January 2012 by terrorists who had previously fought in Iraq, including its chief Abu Mohamed al-Jolani.
The group's military chief Abu Hammam al-Shami and several top commanders were last week reported to have been killed in Syria, although there was contradictory information on the circumstances.